Mark Dominus describes his method of finding and ranking anagrams in this post:
This gave me the idea to score a pair of anagrams according to how many chunks one had to be cut into in order to rearrange it to make the other one. On this plan, the “cholecystoduodenostomy / duodenocholecystostomy” pair would score 3, just barely above the minimum possible score of 2. Something even a tiny bit more interesting, say “abler / blare” would score higher, in this case 4. Even if this strategy didn’t lead me directly to the most interesting anagrams, it would be a big step in the right direction, allowing me to eliminate the least interesting.
This rule would judge both “aal / ala” and “zolotink / zolotnik” as being uninteresting (scores 2 and 4 respectively), which is a good outcome. Note that some other boring-anagram problems can be seen as special cases of this one. For example, short anagrams never need to be cut into many parts: no four-letter anagrams can score higher than 4. The trivial anagramming of a word to itself always scores 1, and nontrivial anagrams always score more than this.
So what we need to do is: for each anagram pair, say acrididae (grasshoppers) and cidaridae (sea urchins), find the smallest number of chunks into which we can chop acrididae so that the chunks can be rearranged into cidaridae.
You can read further details at the link, as well as seeing other candidates; his pick for the single best anagram in English is cinematographer / megachiropteran: “It is 15 letters long, and the only letters that stay together are the E and the R. “Cinematographer” is as familiar as a 15-letter word can be, and “megachiropteran” means a giant bat. GIANT BAT! DEATH FROM ABOVE!!!”